The pension company is unfortunately probably right about this one. Most pension plans are legally required to pay out to whoever's listed as the beneficiary on file, regardless of what the will says or how life circumstances changed. It's one of those things that trips a lot of people up - the will controls your house, your car, your bank accounts, but beneficiary designations on pensions and life insurance bypass all that and go straight to whoever's named.
That said, you do have some options worth exploring. First, check if your dad's pension plan has any appeal or dispute process - some employers will review cases if there's evidence of fraud, coercion, or a really compelling circumstance, though these are rare wins. More importantly, consult with an estate attorney in your state, because laws vary a lot on this. Some states have procedures to challenge outdated beneficiary designations, especially if there's documentation showing your dad intended to change it but died before he could (like draft paperwork or emails). An attorney can also tell you if there's any angle specific to your dad's pension plan or state law that might help.
You might also want to reach out to your dad's employer directly, not just the pension administrator. Sometimes the HR department can provide context or escalate things differently than the standard pension office would. It's worth a conversation even if it seems like a long shot.